Cargando…

Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis

In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and o...

Descripción completa

Detalles Bibliográficos
Autores principales: Öhrman, Caroline, Sahl, Jason W., Sjödin, Andreas, Uneklint, Ingrid, Ballard, Rebecca, Karlsson, Linda, McDonough, Ryelan F., Sundell, David, Soria, Kathleen, Bäckman, Stina, Chase, Kitty, Brindefalk, Björn, Sozhamannan, Shanmuga, Vallesi, Adriana, Hägglund, Emil, Ramirez-Paredes, Jose Gustavo, Thelaus, Johanna, Colquhoun, Duncan, Myrtennäs, Kerstin, Birdsell, Dawn, Johansson, Anders, Wagner, David M., Forsman, Mats
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826819/
https://www.ncbi.nlm.nih.gov/pubmed/33440900
http://dx.doi.org/10.3390/microorganisms9010146
_version_ 1783640611525492736
author Öhrman, Caroline
Sahl, Jason W.
Sjödin, Andreas
Uneklint, Ingrid
Ballard, Rebecca
Karlsson, Linda
McDonough, Ryelan F.
Sundell, David
Soria, Kathleen
Bäckman, Stina
Chase, Kitty
Brindefalk, Björn
Sozhamannan, Shanmuga
Vallesi, Adriana
Hägglund, Emil
Ramirez-Paredes, Jose Gustavo
Thelaus, Johanna
Colquhoun, Duncan
Myrtennäs, Kerstin
Birdsell, Dawn
Johansson, Anders
Wagner, David M.
Forsman, Mats
author_facet Öhrman, Caroline
Sahl, Jason W.
Sjödin, Andreas
Uneklint, Ingrid
Ballard, Rebecca
Karlsson, Linda
McDonough, Ryelan F.
Sundell, David
Soria, Kathleen
Bäckman, Stina
Chase, Kitty
Brindefalk, Björn
Sozhamannan, Shanmuga
Vallesi, Adriana
Hägglund, Emil
Ramirez-Paredes, Jose Gustavo
Thelaus, Johanna
Colquhoun, Duncan
Myrtennäs, Kerstin
Birdsell, Dawn
Johansson, Anders
Wagner, David M.
Forsman, Mats
author_sort Öhrman, Caroline
collection PubMed
description In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.
format Online
Article
Text
id pubmed-7826819
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-78268192021-01-25 Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis Öhrman, Caroline Sahl, Jason W. Sjödin, Andreas Uneklint, Ingrid Ballard, Rebecca Karlsson, Linda McDonough, Ryelan F. Sundell, David Soria, Kathleen Bäckman, Stina Chase, Kitty Brindefalk, Björn Sozhamannan, Shanmuga Vallesi, Adriana Hägglund, Emil Ramirez-Paredes, Jose Gustavo Thelaus, Johanna Colquhoun, Duncan Myrtennäs, Kerstin Birdsell, Dawn Johansson, Anders Wagner, David M. Forsman, Mats Microorganisms Article In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters. MDPI 2021-01-11 /pmc/articles/PMC7826819/ /pubmed/33440900 http://dx.doi.org/10.3390/microorganisms9010146 Text en © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Öhrman, Caroline
Sahl, Jason W.
Sjödin, Andreas
Uneklint, Ingrid
Ballard, Rebecca
Karlsson, Linda
McDonough, Ryelan F.
Sundell, David
Soria, Kathleen
Bäckman, Stina
Chase, Kitty
Brindefalk, Björn
Sozhamannan, Shanmuga
Vallesi, Adriana
Hägglund, Emil
Ramirez-Paredes, Jose Gustavo
Thelaus, Johanna
Colquhoun, Duncan
Myrtennäs, Kerstin
Birdsell, Dawn
Johansson, Anders
Wagner, David M.
Forsman, Mats
Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title_full Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title_fullStr Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title_full_unstemmed Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title_short Reorganized Genomic Taxonomy of Francisellaceae Enables Design of Robust Environmental PCR Assays for Detection of Francisella tularensis
title_sort reorganized genomic taxonomy of francisellaceae enables design of robust environmental pcr assays for detection of francisella tularensis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826819/
https://www.ncbi.nlm.nih.gov/pubmed/33440900
http://dx.doi.org/10.3390/microorganisms9010146
work_keys_str_mv AT ohrmancaroline reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT sahljasonw reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT sjodinandreas reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT uneklintingrid reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT ballardrebecca reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT karlssonlinda reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT mcdonoughryelanf reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT sundelldavid reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT soriakathleen reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT backmanstina reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT chasekitty reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT brindefalkbjorn reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT sozhamannanshanmuga reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT vallesiadriana reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT hagglundemil reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT ramirezparedesjosegustavo reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT thelausjohanna reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT colquhounduncan reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT myrtennaskerstin reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT birdselldawn reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT johanssonanders reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT wagnerdavidm reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis
AT forsmanmats reorganizedgenomictaxonomyoffrancisellaceaeenablesdesignofrobustenvironmentalpcrassaysfordetectionoffrancisellatularensis